Related papers: ERA: Efficient Serial and Parallel Suffix Tree Con…

Parallel surrogate optimization algorithms have proven to be efficient methods for solving expensive noisy optimization problems. In this work we develop a new parallel surrogate optimization algorithm (ProSRS), using a novel tree-based…

We present several results about position heaps, a relatively new alternative to suffix trees and suffix arrays. First, we show that, if we limit the maximum length of patterns to be sought, then we can also limit the height of the heap and…

Genome sequence alignment is the core of many biological applications. The advancement of sequencing technologies produces a tremendous amount of data, making sequence alignment a critical bottleneck in bioinformatics analysis. The existing…

Retrieval-augmented generation (RAG) systems commonly improve robustness via query-time adaptations such as query expansion and iterative retrieval. While effective, these approaches are inherently stateless: adaptations are recomputed for…

Suffix sort plays a critical role in various computational algorithms including genomics as well as in frequently used day to day software applications. The sorting algorithm becomes tricky when we have lot of repeated characters in the…

We present first algorithmic ideas for a practical and lightweight adaption of the DCX suffix array construction algorithm [Sanders et al., 2003] to the distributed-memory setting. Our approach relies on a bucketing technique which enables…

Augmented B-trees (aB-trees) are a broad class of data structures. The seminal work "succincter" by Patrascu showed that any aB-tree can be stored using only two bits of redundancy, while supporting queries to the tree in time proportional…

Finding cohesive subgraphs in a large graph has many important applications, such as community detection and biological network analysis. Clique is often a too strict cohesive structure since communities or biological modules rarely form as…

Parallelism has become a central concern in modern decoding frameworks aiming to meet stringent throughput and latency requirements. Guessing Random Additive Noise Decoding (GRAND) is a recently proposed decoding paradigm that tests…

We introduce a new, practical method for conducting an exact search in a uni- and bidirectional FM index in $O(1)$ time per step while using $O(\log \sigma * n) + o(\log \sigma * \sigma * n)$ bits of space. This is done by replacing the…

The binary indexed tree, or Fenwick tree, is a data structure that can efficiently update values and calculate prefix sums in an array. It allows both of these operations to be performed in $O(\log_2 N)$ time. Here we present a novel data…

Tree kernels are fundamental tools that have been leveraged in many applications, particularly those based on machine learning for Natural Language Processing tasks. In this paper, we devise a parallel implementation of the sequential…

SCAN (Structural Clustering Algorithm for Networks) is a well-studied, widely used graph clustering algorithm. For large graphs, however, sequential SCAN variants are prohibitively slow, and parallel SCAN variants do not effectively share…

In this work, a new indexing technique of data streams called BSTree is proposed. This technique uses the method of data discretization, SAX [4], to reduce online the dimensionality of data streams. It draws on Btree to build the index and…

Efficient index structures for fast approximate nearest neighbor queries are required in many applications such as recommendation systems. In high-dimensional spaces, many conventional methods suffer from excessive usage of memory and slow…

The memory capacity in edge devices is often limited due to constraints on cost, size, and power. Consequently, memory competition leads to inevitable page swapping in memory-constrained mixed-criticality edge devices, causing slow storage…

This paper focuses on reducing memory usage in enumerative model checking, while maintaining the multi-core scalability obtained in earlier work. We present a tree-based multi-core compression method, which works by leveraging sharing among…

Sorting is a fundamental algorithmic pre-processing technique which often allows to represent data more compactly and, at the same time, speeds up search queries on it. In this paper, we focus on the well-studied problem of sorting and…

We show how to build several data structures of central importance to string processing, taking as input the Burrows-Wheeler transform (BWT) and using small extra working space. Let $n$ be the text length and $\sigma$ be the alphabet size.…

In this paper, we present a new data structure called the packed compact trie (packed c-trie) which stores a set $S$ of $k$ strings of total length $n$ in $n \log\sigma + O(k \log n)$ bits of space and supports fast pattern matching queries…